Saman
I think ntr will be the best solution for you. I suggest you to try
with a weak restraint, such as 5 kcal/mol.A² and increase this value
if the system moves too much. You also might have a view of the
restraint energy in the output file.
Hope this will help
Regards
Florent
On Tue, 26 Jul 2016 10:30:54 +0000 (UTC)
Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
> Dear Florent,
> Thank you for your prompt response, actually I want to fix one part
>of my target protein (chain D) except its c terminus residue along
>with another part of my target (chain A). I have attached image here,
>in which red color highlight the active site of chain A and one
>residue from chain D which is located close to its active site. In
>this case, which one is better option to fix specific part of protein
>ntr or ibelly?
> Thanks in advance.
> Best Regards, Saman Yousuf Ali
>
>
> Show original message On Tuesday, July 26, 2016 3:13 PM,
>Barbault Florent <florent.barbault.univ-paris-diderot.fr> wrote:
>
>
> Dear Saman,
>
> Yes it is true, harmonic restraints (ntr) should be the unique
> solution when you want to fix coordinates. However, in some few
>cases
> I find belly useful like when I do simulations of biosensors (a DNA
> linked to a metalic surface, for example). If you work with
>isotropic
> conditions with "classical" atoms you might only need ntr.
>
> Best,
>Florent
>
>
>
> On Tue, 26 Jul 2016 09:38:42 +0000 (UTC)
> Saman Yousuf ali <saman.yousufali64.yahoo.com> wrote:
>> Dear all,
>> Is it true that the use of ntr is better than ibelly to completely
>>freeze certain groups during molecular dynamics simulation?
>>
>> Best Regards, Saman
>>
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>
> -------------------------------------------------
> Dr Florent Barbault
> Maitre de conferences / Associate professor
>
> Universite Paris Diderot
> Laboratoire ITODYS
> 15 rue Jean de Baïf, bâtiment Lavoisier
> 75013 Paris FRANCE
> http://florentbarbault.wordpress.com/
> tel : (33) 01-57-27-68-61
> e-mail : florent.barbault.univ-paris-diderot.fr
> -------------------------------------------------
>
>
>
-------------------------------------------------
Dr Florent Barbault
Maitre de conferences / Associate professor
Universite Paris Diderot
Laboratoire ITODYS
15 rue Jean de Baïf, bâtiment Lavoisier
75013 Paris FRANCE
http://florentbarbault.wordpress.com/
tel : (33) 01-57-27-68-61
e-mail : florent.barbault.univ-paris-diderot.fr
-------------------------------------------------
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Received on Tue Jul 26 2016 - 04:00:03 PDT
